| Package | Maintainer | Title |
|---|---|---|
| ACME | Sean Davis | Algorithms for Calculating Microarray Enrichment (ACME) |
| adSplit | Claudio Lottaz | Annotation-Driven Clustering |
| affyContam | V. Carey | structured corruption of affymetrix cel file data |
| AffyExpress | Xuejun Arthur Li | Affymetrix Quality Assessment and Analysis Tool |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| arrayMvout | V. Carey | multivariate outlier detection for expression array QA |
| ArrayTools | Arthur Li | geneChip Analysis Package |
| BAC | Raphael Gottardo | Bayesian Analysis of Chip-chip experiment |
| BCRANK | Adam Ameur | Predicting binding site consensus from ranked DNA sequences |
| bgafun | Iain Wallace | BGAfun A method to identify specifity determining residues in protein families |
| BGmix | Alex Lewin | Bayesian models for differential gene expression |
| BicARE | Pierre Gestraud , | BicARE |
| Biobase | Biocore Team c/o BioC user list | Biobase: Base functions for Bioconductor |
| BiocCaseStudies | Biocore Team c/o BioC user list | BiocCaseStudies: Support for the Case Studies Monograph |
| bioDist | Biocore Team c/o BioC user list | Different distance measures |
| Biostrings | H. Pages | String objects representing biological sequences, and matching algorithms |
| Category | Robert Gentleman | Category Analysis |
| ChemmineR | Y. Eddie Cao | A Compound Data Mining Framework |
| clusterStab | James W. MacDonald | Compute cluster stability scores for microarray data |
| CMA | Martin Slawski | Synthesis of microarray-based classification |
| CoCiteStats | R. Gentleman | Different test statistics based on co-citation. |
| CORREP | Dongxiao Zhu | Multivariate Correlation Estimator and Statistical Inference Procedures. |
| cosmo | Oliver Bembom | Supervised detection of conserved motifs in DNA sequences |
| cosmoGUI | Oliver Bembom | GUI for constructing constraint sets used by the cosmo package |
| ctc | Antoine Lucas | Cluster and Tree Conversion. |
| daMA | Jobst Landgrebe | Efficient design and analysis of factorial two-colour microarray data |
| DEDS | Yuanyuan Xiao | Differential Expression via Distance Summary for Microarray Data |
| DFP | Rodrigo Alvarez-Glez | Gene Selection |
| diffGeneAnalysis | Choudary Jagarlamudi | Performs differential gene expression Analysis |
| domainsignatures | Florian Hahne | Geneset enrichment based on InterPro domain signatures |
| dualKS | Eric J. Kort | Dual KS Discriminant Analysis and Classification |
| edd | Vince Carey | expression density diagnostics |
| edgeR | Mark Robinson | Empirical analysis of digital gene expression data in R |
| exonmap | Crispin Miller | High level analysis of Affymetrix exon array data |
| factDesign | Denise Scholtens | Factorial designed microarray experiment analysis |
| fdrame | Effi Kenigsberg | FDR adjustments of Microarray Experiments (FDR-AME) |
| flowClust | Raphael Gottardo | Clustering for Flow Cytometry |
| gaga | David Rossell | GaGa hierarchical model for microarray data analysis |
| genefilter | Biocore Team c/o BioC user list | genefilter: methods for filtering genes from microarray experiments |
| GeneMeta | Biocore Team c/o BioC user list | MetaAnalysis for High Throughput Experiments |
| geneRecommender | Greg Hather | A gene recommender algorithm to identify genes coexpressed with a query set of genes |
| GeneSelector | Martin Slawski | GeneSelector |
| GGBase | Vince Carey | infrastructure for genetics of gene expression (c) 2008 VJ Carey |
| GGtools | Vince Carey | software and data for genetical genomics (c) 2006 VJ Carey |
| GlobalAncova | R. Meister | Calculates a global test for differential gene expression between groups |
| globaltest | Jelle Goeman | Testing Association of Groups of Genes with a Clinical Variable |
| GOstats | Robert Gentleman | Tools for manipulating GO and microarrays. |
| gpls | Biocore Team c/o BioC user list | Classification using generalized partial least squares |
| GraphAT | Thomas LaFramboise | Graph Theoretic Association Tests |
| GSEABase | Biocore Team c/o BioC user list | Gene set enrichment data structures and methods |
| GSEAlm | Assaf Oron | Linear Model Toolset for Gene Set Enrichment Analysis |
| HEM | HyungJun Cho | Heterogeneous error model for identification of differentially expressed genes under multiple conditions |
| hopach | Katherine S. Pollard | Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) |
| Icens | Biocore Team c/o BioC user list | NPMLE for Censored and Truncated Data |
| impute | Balasubramanian Narasimhan | impute: Imputation for microarray data |
| iterativeBMA | Ka Yee Yeung | The Iterative Bayesian Model Averaging (BMA) algorithm |
| iterativeBMAsurv | Ka Yee Yeung | The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis |
| lapmix | Yann Ruffieux | Laplace Mixture Model in Microarray Experiments |
| LBE | Cyril Dalmasso | Estimation of the false discovery rate. |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| LMGene | John Tillinghast | LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays |
| logicFS | Holger Schwender | Identification of SNP Interactions |
| LPE | Nitin Jain | Methods for analyzing microarray data using Local Pooled Error (LPE) method |
| LPEadj | Carl Murie | A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size. |
| maanova | Hyuna Yang | Tools for analyzing Micro Array experiments |
| made4 | Aedin Culhane | Multivariate analysis of microarray data using ADE4 |
| maigesPack | Gustavo H. Esteves | Functions to handle cDNA microarray data, including several methods of data analysis |
| MantelCorr | Brian Steinmeyer | Compute Mantel Cluster Correlations |
| maSigPro | Ana Conesa | Significant Gene Expression Profile Differeneces in Time Course Microarray Data |
| MeasurementError.cor | Beiying Ding | Measurement Error model estimate for correlation coefficient |
| metaArray | Hyungwon Choi | Integration of Microarray Data for Meta-analysis |
| Mfuzz | Matthias Futschik | Soft clustering of time series gene expression data |
| microRNA | Robert Gentleman | Data and functions for dealing with microRNAs |
| MiPP | Sukwoo Kim | Misclassification Penalized Posterior Classification |
| miRNApath | James M. Ward | miRNApath: Pathway Enrichment for miRNA Expression Data |
| MLInterfaces | V. Carey | Uniform interfaces to R machine learning procedures for data in Bioconductor containers |
| multtest | Katherine S. Pollard | Resampling-based multiple hypothesis testing |
| nem | Florian Markowetz | Nested Effects Models to reconstruct phenotypic hierarchies |
| occugene | Oliver Will | Functions for Multinomial Occupancy Distribution |
| OCplus | Alexander Ploner | Operating characteristics plus sample size and local fdr for microarray experiments |
| oneChannelGUI | Raffaele A Calogero | This package extends the capabilities of affylmGUI graphical interface. Affymetrix 3' IVT, gene an exon arrays are actually implemented togheter with Illumina, GEO matrix series files and tab delimited files. |
| OrderedList | Claudio Lottaz | Similarities of Ordered Gene Lists |
| OutlierD | Sukwoo Kim | Outlier detection using quantile regression on the M-A scatterplots of high-throughput data |
| pamr | Rob Tibshirani | Pam: prediction analysis for microarrays |
| parody | VJ Carey | Parametric And Resistant Outlier DYtection |
| pcaMethods | Wolfram Stacklies | A collection of PCA methods. |
| pdmclass | James W. MacDonald | Classification of Microarray Samples using Penalized Discriminant Methods |
| plw | Magnus Astrand | Probe level Locally moderated Weighted t-tests. |
| puma | Richard Pearson | Propagating Uncertainty in Microarray Analysis |
| qvalue | John D. Storey | Q-value estimation for false discovery rate control |
| rbsurv | Sooheang Eo | Robust likelihood-based survival modeling with microarray data |
| rflowcyt | N. LeMeur | Statistical tools and data structures for analytic flow cytometry |
| rHVDM | Martino Barenco | Hidden Variable Dynamic Modeling |
| RNAither | Nora Rieber | Statistical analysis of high-throughput RNAi screens |
| ROC | Vince Carey | utilities for ROC, with uarray focus |
| Rtreemix | Jasmina Bogojeska | Rtreemix: Mutagenetic trees mixture models. |
| SAGx | Per Broberg, | Statistical Analysis of the GeneChip |
| seqLogo | Oliver Bembom | Sequence logos for DNA sequence alignments |
| sigPathway | Weil Lai | Pathway Analysis |
| SIM | Maarten van Iterson | Integrated Analysis of gene expression and copynumber data |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| sizepower | Weiliang Qiu | Sample Size and Power Calculation in Micorarray Studies |
| SLqPCR | Matthias Kohl | Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH |
| sscore | Richard Kennedy | S-Score Algorithm for Affymetrix Oligonucleotide Microarrays |
| ssize | Gregory R. Warnes | Estimate Microarray Sample Size |
| stam | Claudio Lottaz | Structured Analysis of Microarray Data |
| timecourse | Yu Chuan Tai | Statistical Analysis for Developmental Microarray Time Course Data |
| topGO | Adrian Alexa | topGO: Enrichment analysis for Gene Ontology |
| twilight | Stefanie Scheid | Estimation of local false discovery rate |
| VanillaICE | Robert Scharpf | Methods for fitting Hidden Markov Models to SNP chip data |
| vbmp | Nicola Lama | Variational Bayesian Multinomial Probit Regression |
| XDE | Robert Scharpf | XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression |